PGS Catalog - PGS000123 / Parkinson's disease (Polygenic Score)

Polygenic Score (PGS) ID: PGS000123

Predicted Trait
Reported Trait	Parkinson's disease
Mapped Trait(s)	Parkinson disease (MONDO_0005180)

Released in PGS Catalog: March 27, 2020

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Score Details

Score Construction
PGS Name	2017_PD16
Development Method
Name	Genome-wide significant variants
Parameters	The PRS was computed using the binary logarithm transformation of the reported ORs
Variants
Original Genome Build	NR
Number of Variants	16
Effect Weight Type	Log2(OR)

PGS Source
PGS Catalog Publication (PGP) ID	PGP000059
Citation (link to publication)	Ibanez L et al. BMC Neurol (2017)

Ancestry Distribution
Source of Variant Associations (GWAS)	European: 100% 108,990 individuals (100%)
PGS Evaluation	European: 100% 2 Sample Sets

Development Samples

Source of Variant Associations (GWAS)

Study Identifiers	Sample Numbers	Sample Ancestry	Cohort(s)
GWAS Catalog: GCST002544 Europe PMC: 25064009	108,990 individuals	European	NR

Performance Metrics

Disclaimer: The performance metrics are displayed as reported by the source studies. It is important to note that metrics are not necessarily comparable with each other. For example, metrics depend on the sample characteristics (described by the PGS Catalog Sample Set [PSS] ID), phenotyping, and statistical modelling. Please refer to the source publication for additional guidance on performance.

PGS Performance Metric ID (PPM)	PGS Sample Set ID (PSS)	Performance Source	Trait	PGS Effect Sizes (per SD change)	Classification Metrics	Other Metrics	Covariates Included in the Model	PGS Performance: Other Relevant Information
PPM000398	PSS000226\| European Ancestry\| 786 individuals	PGP000059 \| Ibanez L et al. BMC Neurol (2017)	Reported Trait: Age at Onset (Survival)	β: 9.3 [3.59, 15.0]	—	Association (p-value): 0.00141	age at last assessment, sex, 2 PCs of ancestry	Cox regression
PPM000396	PSS000225\| European Ancestry\| 469 individuals	PGP000059 \| Ibanez L et al. BMC Neurol (2017)	Reported Trait: Age at Onset (Survival)	β: 16.62 [9.63, 23.61]	—	Association (p-value): 3.19e-06	age at last assessment, sex, 2 PCs of ancestry	Cox regression
PPM000397	PSS000226\| European Ancestry\| 786 individuals	PGP000059 \| Ibanez L et al. BMC Neurol (2017)	Reported Trait: Parkinson disease	β: 4.85 [2.32, 7.39]	—	Association (p-value): 0.00018	age at last assessment, sex, 2 PCs of ancestry	—
PPM000395	PSS000225\| European Ancestry\| 469 individuals	PGP000059 \| Ibanez L et al. BMC Neurol (2017)	Reported Trait: Parkinson disease	β: 5.84 [3.1, 8.59]	—	Association (p-value): 3e-05	age at last assessment, sex, 2 PCs of ancestry	—

Evaluated Samples

PGS Sample Set ID (PSS)	Phenotype Definitions and Methods	Participant Follow-up Time	Sample Numbers	Age of Study Participants	Sample Ancestry	Additional Ancestry Description	Cohort(s)	Additional Sample/Cohort Information
PSS000226	—	—	786 individuals [ 493 cases , 293 controls ] , 58.27 % Male samples	—	European	—	WUSTL	Both the PPMI and WUSTL datasets are available by request from the PPMI website (www.ppmi-info.org)
PSS000225	—	—	469 individuals [ 334 cases , 135 controls ] , 55.22 % Male samples	—	European	—	PPMI	Both the PPMI and WUSTL datasets are available by request from the PPMI website (www.ppmi-info.org)